From 75a047e9cf73abf7467fd8fc2d1d5f961ee55505 Mon Sep 17 00:00:00 2001
From: Sebastian Ehlert <28669218+awvwgk@users.noreply.github.com>
Date: Thu, 19 Nov 2020 17:30:47 +0100
Subject: [PATCH] Allow to create PDB specific filters

---
 app/main.f90         | 18 ++++++++++++++----
 fpm.toml             |  2 +-
 man/mctc-rmsd.1.adoc |  9 +++++++++
 meson.build          |  2 +-
 src/rmsd/filter.f90  | 26 +++++++++++++++++++++++---
 src/rmsd/version.f90 |  4 ++--
 6 files changed, 50 insertions(+), 11 deletions(-)

diff --git a/app/main.f90 b/app/main.f90
index 3c63a80..e3f1457 100644
--- a/app/main.f90
+++ b/app/main.f90
@@ -58,13 +58,14 @@ program rmsd_main
    call get_value(opts, "help", show_help, size(args) <= 1 .and. .not.show_rc)
    call opts%destroy
 
-   if (show_help) then
-      call help(output_unit)
+   if (show_version) then
+      call version(output_unit)
       stop
    end if
 
-   if (show_version) then
-      call version(output_unit)
+   if (show_help) then
+      call help(output_unit)
+      if (size(args) <= 1) error stop
       stop
    end if
 
@@ -212,6 +213,15 @@ subroutine help(unit)
       "", &
       "Note that this approach will still consider deuterium labeled as D,", &
       "which would be excluded as well when using the atomic number instead.", &
+      "", &
+      "To create a PDB specific filter use the four character PDB identifier", &
+      "of the atoms and enable the PDB functionality.", &
+      "To match only the proteine backbone use", &
+      "", &
+      "    c-alpha.include = ["" CA "", "" N  "", "" C  "", "" O  ""]", &
+      "    c-alpha.pdb = true", &
+      "", &
+      "Atomic numbers and element symbols can be included here as well.", &
       ""
 
 end subroutine help
diff --git a/fpm.toml b/fpm.toml
index 7448e04..4dc6e7e 100644
--- a/fpm.toml
+++ b/fpm.toml
@@ -1,5 +1,5 @@
 name = "mctc-rmsd"
-version = "0.1.0"
+version = "0.1.1"
 license = "LGPL-3.0-or-later"
 
 [dependencies]
diff --git a/man/mctc-rmsd.1.adoc b/man/mctc-rmsd.1.adoc
index a6761d3..0ba0ac4 100644
--- a/man/mctc-rmsd.1.adoc
+++ b/man/mctc-rmsd.1.adoc
@@ -54,3 +54,12 @@ excluding hydrogen with standard symbols, use:
 
 Note that this approach will still consider deuterium labeled as D,
 which would be excluded as well when using the atomic number instead.
+
+To create a PDB specific filter use the four character PDB identifier
+of the atoms and enable the PDB functionality.
+To match only the proteine backbone use
+
+    backbone.include = [" CA ", " N  ", " C  ", " O  "]
+    backbone.pdb = true
+
+Atomic numbers and element symbols can be included here as well.
diff --git a/meson.build b/meson.build
index 6cea90e..df8ad48 100644
--- a/meson.build
+++ b/meson.build
@@ -16,7 +16,7 @@
 project(
   'mctc-rmsd',
   'fortran',
-  version: '0.1.0',
+  version: '0.1.1',
   license: 'LGPL-3.0-or-later',
   meson_version: '>=0.53',
   default_options: [
diff --git a/src/rmsd/filter.f90 b/src/rmsd/filter.f90
index 665cd50..e63291d 100644
--- a/src/rmsd/filter.f90
+++ b/src/rmsd/filter.f90
@@ -42,6 +42,9 @@ module rmsd_filter
       !> Whether the filter contains an allow or a deny list
       logical :: allow
 
+      !> Use PDB identifiers for filtering
+      logical :: pdb
+
    contains
 
       !> Create mask from filter and structure
@@ -112,10 +115,11 @@ subroutine new_rmsd_filter_tbl(self, table, error)
    character(symbol_length), allocatable :: sym(:)
    character(len=:), allocatable :: name, cval
    integer :: ndim, inum, isym, ival, i, stat
-   logical :: allow
+   logical :: allow, pdb
 
    call table%get_key(name)
 
+   call get_value(table, "pdb", pdb, .false.)
    call get_value(table, "include", array, requested=.false.)
    allow = associated(array)
    if (.not.allow) then
@@ -159,13 +163,13 @@ subroutine new_rmsd_filter_tbl(self, table, error)
    if (allocated(error)) return
 
    call new_rmsd_filter(self, name=name, num=num(:inum), sym=sym(:isym), &
-      & allow=allow)
+      & allow=allow, pdb=pdb)
 
 end subroutine new_rmsd_filter_tbl
 
 
 !> Create a new RMSD filter from parts
-subroutine new_rmsd_filter_one(self, name, num, sym, allow)
+subroutine new_rmsd_filter_one(self, name, num, sym, allow, pdb)
 
    !> Instance of species filter
    type(rmsd_filter_type), intent(out) :: self
@@ -176,6 +180,9 @@ subroutine new_rmsd_filter_one(self, name, num, sym, allow)
    !> Whether the filter contains an allow or a deny list
    logical, intent(in) :: allow
 
+   !> Filter is specific for PDB identifiers
+   logical, intent(in) :: pdb
+
    !> Atomic number
    integer, intent(in) :: num(:)
 
@@ -186,6 +193,7 @@ subroutine new_rmsd_filter_one(self, name, num, sym, allow)
    self%sym = sym
    self%num = num
    self%allow = allow
+   self%pdb = pdb
 
 end subroutine new_rmsd_filter_one
 
@@ -224,6 +232,18 @@ subroutine get_mask(self, mol, mask)
       izp = mol%id(iat)
       mask(iat) = tmp(izp)
    end do
+
+   if (self%pdb .and. allocated(mol%pdb)) then
+      if (self%allow) then
+         do iat = 1, mol%nat
+            mask(iat) = mask(iat) .or. any(mol%pdb(iat)%name == self%sym)
+         end do
+      else
+         do iat = 1, mol%nat
+            mask(iat) = mask(iat) .and. all(mol%pdb(iat)%name /= self%sym)
+         end do
+      end if
+   end if
       
 end subroutine get_mask
 
diff --git a/src/rmsd/version.f90 b/src/rmsd/version.f90
index b37c68e..cf11c91 100644
--- a/src/rmsd/version.f90
+++ b/src/rmsd/version.f90
@@ -23,10 +23,10 @@ module rmsd_version
 
 
    !> String representation of the mctc-rmsd version
-   character(len=*), parameter :: rmsd_version_string = "0.1.0"
+   character(len=*), parameter :: rmsd_version_string = "0.1.1"
 
    !> Numeric representation of the mctc-rmsd version
-   integer, parameter :: rmsd_version_compact(3) = [0, 1, 0]
+   integer, parameter :: rmsd_version_compact(3) = [0, 1, 1]
 
 
 contains